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2. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies.

Author

Li, Yun, van Setten, Jessica, Verma, Shefali, Lu, Yontao, Holmes, Michael, Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad, Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael, Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey, McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain, Al-Ali, Amein, Al-Muhanna, Fahad, Al-Rubaish, Abdullah, Al-Mueilo, Samir, Monos, Dimitri, Murphy, Barbara, Olthoff, Kim, Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew, Oetting, William, Garcia-Pavia, Pablo, MacArthur, Daniel, de Bakker, Paul, Hakonarson, Hakon, Birdwell, Kelly, Jacobson, Pamala, Ritchie, Marylyn, Asselbergs, Folkert, Israni, Ajay, Shaked, Abraham, and Keating, Brendan

Subjects
DNA Copy Number Variations, Genome-Wide Association Study, Genotype, HLA Antigens, Humans, Polymorphism, Single Nucleotide, Receptors, KIR
Abstract

BACKGROUND: In addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation. METHODS: We describe here the design and implementation of a customized genome-wide genotyping array, the TxArray, comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios. RESULTS: We show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms. CONCLUSIONS: We have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

Published
2015

3. Genotyping Informatics and Quality Control for 100,000 Subjects in the Genetic Epidemiology Research on Adult Health and Aging (GERA) Cohort.

Author

Kvale, Mark N, Hesselson, Stephanie, Hoffmann, Thomas J, Cao, Yang, Chan, David, Connell, Sheryl, Croen, Lisa A, Dispensa, Brad P, Eshragh, Jasmin, Finn, Andrea, Gollub, Jeremy, Iribarren, Carlos, Jorgenson, Eric, Kushi, Lawrence H, Lao, Richard, Lu, Yontao, Ludwig, Dana, Mathauda, Gurpreet K, McGuire, William B, Mei, Gangwu, Miles, Sunita, Mittman, Michael, Patil, Mohini, Quesenberry, Charles P, Ranatunga, Dilrini, Rowell, Sarah, Sadler, Marianne, Sakoda, Lori C, Shapero, Michael, Shen, Ling, Shenoy, Tanu, Smethurst, David, Somkin, Carol P, Van Den Eeden, Stephen K, Walter, Lawrence, Wan, Eunice, Webster, Teresa, Whitmer, Rachel A, Wong, Simon, Zau, Chia, Zhan, Yiping, Schaefer, Catherine, Kwok, Pui-Yan, and Risch, Neil

Subjects
Humans, Oligonucleotide Array Sequence Analysis, Cohort Studies, Computational Biology, Aging, Polymorphism, Single Nucleotide, Quality Control, Adult, Health, Female, Male, Molecular Epidemiology, Genotyping Techniques, Affymetrix Axiom, GERA cohort, genome-wide genotyping, quality control, saliva DNA, Genetics, Human Genome, Generic health relevance, Developmental Biology
Abstract

The Kaiser Permanente (KP) Research Program on Genes, Environment and Health (RPGEH), in collaboration with the University of California-San Francisco, undertook genome-wide genotyping of >100,000 subjects that constitute the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort. The project, which generated >70 billion genotypes, represents the first large-scale use of the Affymetrix Axiom Genotyping Solution. Because genotyping took place over a short 14-month period, creating a near-real-time analysis pipeline for experimental assay quality control and final optimized analyses was critical. Because of the multi-ethnic nature of the cohort, four different ethnic-specific arrays were employed to enhance genome-wide coverage. All assays were performed on DNA extracted from saliva samples. To improve sample call rates and significantly increase genotype concordance, we partitioned the cohort into disjoint packages of plates with similar assay contexts. Using strict QC criteria, the overall genotyping success rate was 103,067 of 109,837 samples assayed (93.8%), with a range of 92.1-95.4% for the four different arrays. Similarly, the SNP genotyping success rate ranged from 98.1 to 99.4% across the four arrays, the variation depending mostly on how many SNPs were included as single copy vs. double copy on a particular array. The high quality and large scale of genotype data created on this cohort, in conjunction with comprehensive longitudinal data from the KP electronic health records of participants, will enable a broad range of highly powered genome-wide association studies on a diversity of traits and conditions.

Published
2015

4. Probe Selection for High-Density Oligonucleotide Arrays

Author

Mei, Rui, Hubbell, Earl, Bekiranov, Stefan, Mittmann, Mike, Christians, Fred C., Shen, Mei-Mei, Lu, Gang, Fang, Joy, Liu, Wei-Min, Ryder, Tom, Kaplan, Paul, Kulp, David, and Webster, Teresa A.

Published
2003

5. Novel genotyping algorithms for rare variants significantly improve the accuracy of Applied Biosystems™ Axiom™ array genotyping calls: Retrospective evaluation of UK Biobank array data

Author

Mizrahi-Man, Orna, primary, Woehrmann, Marcos H., additional, Webster, Teresa A., additional, Gollub, Jeremy, additional, Bivol, Adrian, additional, Keeble, Sara M., additional, Aull, Katherine H., additional, Mittal, Anuradha, additional, Roter, Alan H., additional, Wong, Brant A., additional, and Schmidt, Jeanette P., additional

Published
2022
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7. A global reference for human genetic variation

Author

Altshuler, David M., (Co-Chair), Durbin, Richard M., (Co-Chair, Principal Investigator), Donnelly, Peter, Green, Eric D., Nickerson, Deborah A., Boerwinkle, Eric, Doddapaneni, Harsha, Han, Yi, Korchina, Viktoriya, Kovar, Christie, Lee, Sandra, Muzny, Donna, Reid, Jeffrey G., Zhu, Yiming, Wang, Jun, (Principal Investigator), Chang, Yuqi, Feng, Qiang, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Lan, Tianming, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Liu, Shengmao, Liu, Xiao, Lu, Yao, Ma, Xuedi, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Xu, Xun, Yin, Ye, Zhang, Dandan, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Lander, Eric S., (Principal Investigator), Gabriel, Stacey B., (Co-Chair), Gupta, Namrata, Gharani, Neda, Toji, Lorraine H., Gerry, Norman P., Resch, Alissa M., Barker, Jonathan, Gil, Laurent, Hunt, Sarah E., Kelman, Gavin, Kulesha, Eugene, Leinonen, Rasko, McLaren, William M., Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Smith, Richard E., Streeter, Ian, Thormann, Anja, Toneva, Iliana, Vaughan, Brendan, Zheng-Bradley, Xiangqun, Bentley, David R., (Principal Investigator), Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, (Principal Investigator), Sudbrak, Ralf, (Project Leader), Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Mardis, Elaine R., (Co-Principal Investigator) (Co-Chair), Wilson, Richard K., (Co-Principal Investigator), Fulton, Lucinda, Fulton, Robert, Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Church, Deanna, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, O’Sullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., (Principal Investigator), Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, (Principal Investigator), Campbell, Christopher L., Kong, Yu, Marcketta, Anthony, Yu, Fuli, (Project Leader), Antunes, Lilian, Bainbridge, Matthew, Sabo, Aniko, Huang, Zhuoyi, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Shao, Haojing, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Alkan, Can, Dal, Elif, Kahveci, Fatma, Garrison, Erik P., (Project Lead), Kural, Deniz, Lee, Wan-Ping, Leong, Wen Fung, Stromberg, Michael, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Daly, Mark J., (Principal Investigator), DePristo, Mark A., (Project Leader), Handsaker, Robert E., (Project Leader), Banks, Eric, Bhatia, Gaurav, del Angel, Guillermo, Genovese, Giulio, Li, Heng, Kashin, Seva, Nemesh, James C., Poplin, Ryan E., Yoon, Seungtai C., (Principal Investigator), Lihm, Jayon, Makarov, Vladimir, Clark, Andrew G., (Principal Investigator), Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Rausch, Tobias, (Project Leader), Fritz, Markus H., Stütz, Adrian M., Beal, Kathryn, Datta, Avik, Herrero, Javier, Ritchie, Graham R. S., Zerbino, Daniel, Sabeti, Pardis C., (Principal Investigator), Shlyakhter, Ilya, Schaffner, Stephen F., Vitti, Joseph, Cooper, David N., (Principal Investigator), Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Cheetham, Keira R., Cox, Anthony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Kenny, Eimear E., (Principal Investigator), Batzer, Mark A., (Principal Investigator), Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., (Principal Investigator), Lek, Monkol, Herwig, Ralf, Koboldt, Daniel C., Larson, David, Ye, Kai, Gravel, Simon, Swaroop, Anand, Chew, Emily, Lappalainen, Tuuli, (Principal Investigator), Erlich, Yaniv, (Principal Investigator), Gymrek, Melissa, Willems, Thomas Frederick, Simpson, Jared T., Shriver, Mark D., (Principal Investigator), Rosenfeld, Jeffrey A., (Principal Investigator), Montgomery, Stephen B., (Principal Investigator), De La Vega, Francisco M., (Principal Investigator), Byrnes, Jake K., Carroll, Andrew W., DeGorter, Marianne K., Lacroute, Phil, Maples, Brian K., Martin, Alicia R., Moreno-Estrada, Andres, Shringarpure, Suyash S., Zakharia, Fouad, Halperin, Eran, (Principal Investigator), Baran, Yael, Cerveira, Eliza, Hwang, Jaeho, Malhotra, Ankit, (Co-Project Lead), Plewczynski, Dariusz, Radew, Kamen, Romanovitch, Mallory, Zhang, Chengsheng, (Co-Project Lead), Hyland, Fiona C. L., Craig, David W., (Principal Investigator), Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, (Principal Investigator), Antaki, Danny, Gujral, Madhusudan, Noor, Amina, Ye, Kenny, Burchard, Esteban G., (Principal Investigator), Hernandez, Ryan D., (Principal Investigator), Gignoux, Christopher R., Haussler, David, (Principal Investigator), Katzman, Sol J., Kent, James W., Howie, Bryan, Ruiz-Linares, Andres, (Principal Investigator), Dermitzakis, Emmanouil T., (Principal Investigator), Devine, Scott E., (Principal Investigator), Abecasis, Gonçalo R., (Principal Investigator) (Co-Chair), Kang, Hyun Min, (Project Leader), Kidd, Jeffrey M., (Principal Investigator), Blackwell, Tom, Caron, Sean, Chen, Wei, Emery, Sarah, Fritsche, Lars, Fuchsberger, Christian, Jun, Goo, Li, Bingshan, Lyons, Robert, Scheller, Chris, Sidore, Carlo, Song, Shiya, Sliwerska, Elzbieta, Taliun, Daniel, Tan, Adrian, Welch, Ryan, Wing, Mary Kate, Zhan, Xiaowei, Awadalla, Philip, (Principal Investigator), Hodgkinson, Alan, Li, Yun, Shi, Xinghua, (Principal Investigator), Quitadamo, Andrew, Lunter, Gerton, (Principal Investigator), McVean, Gil A., (Principal Investigator) (Co-Chair), Marchini, Jonathan L., (Principal Investigator), Myers, Simon, (Principal Investigator), Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Kretzschmar, Warren, Iqbal, Zamin, Mathieson, Iain, Menelaou, Androniki, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., (Principal Investigator), Fu, Yunxin, (Principal Investigator), Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, (Principal Investigator), Witherspoon, David, Xing, Jinchuan, Browning, Brian L., (Principal Investigator), Browning, Sharon R., (Principal Investigator), Hormozdiari, Fereydoun, Sudmant, Peter H., Khurana, Ekta, (Principal Investigator), Hurles, Matthew E., (Principal Investigator), Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Colonna, Vincenza, Jostins, Luke, Walter, Klaudia, Xue, Yali, Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Harmanci, Arif O., Jin, Mike, Lee, Donghoon, Liu, Jeremy, Mu, Xinmeng Jasmine, Zhang, Jing, Zhang, Yan, McCarroll, Steven A., (Principal Investigator), Hartl, Chris, Shakir, Khalid, Degenhardt, Jeremiah, Korbel, Jan O., (Principal Investigator) (Co-Chair), Meiers, Sascha, Raeder, Benjamin, Casale, Francesco Paolo, Stegle, Oliver, Lameijer, Eric-Wubbo, Ding, Li, (Principal Investigator), Hall, Ira, Lee, Charles, (Principal Investigator) (Co-Chair), Bafna, Vineet, Michaelson, Jacob, Gardner, Eugene J., (Project Leader), Mills, Ryan E., (Principal Investigator), Dayama, Gargi, Chen, Ken, (Principle Investigator), Fan, Xian, Chong, Zechen, Chen, Tenghui, Eichler, Evan E., (Principal Investigator) (Co-Chair), Chaisson, Mark J., Huddleston, John, Malig, Maika, Nelson, Bradley J., Parrish, Nicholas F., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, Zhang, Yujun, Lam, Hugo, Sisu, Cristina, Gibbs, Richard A., (Principal Investigator) (Co-Chair), Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Yu, Jin, Li, Wangshen, Marth, Gabor T., (Principal Investigator) (Co-Chair), Habegger, Lukas, Yu, Haiyuan, (Principal Investigator), Cunningham, Fiona, Dunham, Ian, Lage, Kasper, (Principal Investigator), Jespersen, Jakob Berg, Horn, Heiko, Tyler-Smith, Chris, (Principal Investigator) (Co-Chair), Gerstein, Mark B., (Principal Investigator) (Co-Chair), Kim, Donghoon, Desalle, Rob, Narechania, Apurva, Wilson Sayres, Melissa A., Bustamante, Carlos D., (Principal Investigator) (Co-Chair), Mendez, Fernando L., Poznik, David G., Underhill, Peter A., Coin, Lachlan, (Principal Investigator), Mittelman, David, Banerjee, Ruby, Cerezo, Maria, Fitzgerald, Thomas W., Louzada, Sandra, Massaia, Andrea, Ritchie, Graham R., Yang, Fengtang, Kalra, Divya, Hale, Walker, Dan, Xu, Flicek, Paul, (Principal Investigator) (Co-Chair), Clarke, Laura, (Project Lead), Sherry, Stephen T., (Principal Investigator) (Co-Chair), Chakravarti, Aravinda, (Co-Chair), Knoppers, Bartha M., (Co-Chair), Barnes, Kathleen C., Beiswanger, Christine, Cai, Hongyu, Cao, Hongzhi, Henn, Brenna, Jones, Danielle, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Tian, Zhongming, Tishkoff, Sarah, Via, Marc, Wang, Yuhong, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Cai, Zhiming, Gao, Yang, Chu, Jiayou, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Mathias, Rasika A., Hennis, Anselm, Watson, Harold, McKenzie, Colin, Qadri, Firdausi, LaRocque, Regina, Deng, Xiaoyan, Asogun, Danny, Folarin, Onikepe, Happi, Christian, Omoniwa, Omonwunmi, Stremlau, Matt, Tariyal, Ridhi, Jallow, Muminatou, Joof, Fatoumatta Sisay, Corrah, Tumani, Rockett, Kirk, Kwiatkowski, Dominic, Kooner, Jaspal, Hiê`n, Trâ`n Tinh, Dunstan, Sarah J., Hang, Nguyen Thuy, Fonnie, Richard, Garry, Robert, Kanneh, Lansana, Moses, Lina, Schieffelin, John, Grant, Donald S., Gallo, Carla, Poletti, Giovanni, Saleheen, Danish, Rasheed, Asif, Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Vaydylevich, Yekaterina, Duncanson, Audrey, Dunn, Michael, Schloss, Jeffery A., and Yang, Huanming

Published
2015
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8. An integrated map of genetic variation from 1,092 human genomes

Author

McVean, Gil A., Altshuler, David M., Durbin, Richard M., Abecasis, Gonçalo R., Bentley, David R., Chakravarti, Aravinda, Clark, Andrew G., Donnelly, Peter, Eichler, Evan E., Flicek, Paul, Gabriel, Stacey B., Gibbs, Richard A., Green, Eric D., Hurles, Matthew E., Knoppers, Bartha M., Korbel, Jan O., Lander, Eric S., Lee, Charles, Lehrach, Hans, Mardis, Elaine R., Marth, Gabor T., Nickerson, Deborah A., Schmidt, Jeanette P., Sherry, Stephen T., Wang, Jun, Wilson, Richard K., Dinh, Huyen, Kovar, Christie, Lee, Sandra, Lewis, Lora, Muzny, Donna, Reid, Jeff, Wang, Min, Wang, Jun, Fang, Xiaodong, Guo, Xiaosen, Jian, Min, Jiang, Hui, Jin, Xin, Li, Guoqing, Li, Jingxiang, Li, Yingrui, Li, Zhuo, Liu, Xiao, Lu, Yao, Ma, Xuedi, Su, Zhe, Tai, Shuaishuai, Tang, Meifang, Wang, Bo, Wang, Guangbiao, Wu, Honglong, Wu, Renhua, Yin, Ye, Zhang, Wenwei, Zhao, Jiao, Zhao, Meiru, Zheng, Xiaole, Zhou, Yan, Lander, Eric S., Gabriel, Stacey B., Gupta, Namrata, Flicek, Paul, Clarke, Laura, Leinonen, Rasko, Smith, Richard E., Zheng-Bradley, Xiangqun, Bentley, David R., Grocock, Russell, Humphray, Sean, James, Terena, Kingsbury, Zoya, Lehrach, Hans, Sudbrak, Ralf, Albrecht, Marcus W., Amstislavskiy, Vyacheslav S., Borodina, Tatiana A., Lienhard, Matthias, Mertes, Florian, Sultan, Marc, Timmermann, Bernd, Yaspo, Marie-Laure, Sherry, Stephen T., McVean, Gil A., Mardis, Elaine R., Wilson, Richard K., Fulton, Lucinda, Fulton, Robert, Weinstock, George M., Durbin, Richard M., Balasubramaniam, Senduran, Burton, John, Danecek, Petr, Keane, Thomas M., Kolb-Kokocinski, Anja, McCarthy, Shane, Stalker, James, Quail, Michael, Schmidt, Jeanette P., Davies, Christopher J., Gollub, Jeremy, Webster, Teresa, Wong, Brant, Zhan, Yiping, Auton, Adam, Yu, Fuli, Bainbridge, Matthew, Challis, Danny, Evani, Uday S., Lu, James, Nagaswamy, Uma, Sabo, Aniko, Wang, Yi, Yu, Jin, Coin, Lachlan J. M., Fang, Lin, Li, Qibin, Li, Zhenyu, Lin, Haoxiang, Liu, Binghang, Luo, Ruibang, Qin, Nan, Shao, Haojing, Wang, Bingqiang, Xie, Yinlong, Ye, Chen, Yu, Chang, Zhang, Fan, Zheng, Hancheng, Zhu, Hongmei, Garrison, Erik P., Kural, Deniz, Lee, Wan-Ping, Fung Leong, Wen, Ward, Alistair N., Wu, Jiantao, Zhang, Mengyao, Lee, Charles, Griffin, Lauren, Hsieh, Chih-Heng, Mills, Ryan E., Shi, Xinghua, von Grotthuss, Marcin, Zhang, Chengsheng, Daly, Mark J., DePristo, Mark A., Banks, Eric, Bhatia, Gaurav, Carneiro, Mauricio O., del Angel, Guillermo, Genovese, Giulio, Handsaker, Robert E., Hartl, Chris, McCarroll, Steven A., Nemesh, James C., Poplin, Ryan E., Schaffner, Stephen F., Shakir, Khalid, Yoon, Seungtai C., Lihm, Jayon, Makarov, Vladimir, Jin, Hanjun, Kim, Wook, Cheol Kim, Ki, Korbel, Jan O., Rausch, Tobias, Beal, Kathryn, Cunningham, Fiona, Herrero, Javier, McLaren, William M., Ritchie, Graham R. S., Clark, Andrew G., Gottipati, Srikanth, Keinan, Alon, Rodriguez-Flores, Juan L., Sabeti, Pardis C., Grossman, Sharon R., Tabrizi, Shervin, Tariyal, Ridhi, Cooper, David N., Ball, Edward V., Stenson, Peter D., Barnes, Bret, Bauer, Markus, Keira Cheetham, R., Cox, Tony, Eberle, Michael, Kahn, Scott, Murray, Lisa, Peden, John, Shaw, Richard, Ye, Kai, Batzer, Mark A., Konkel, Miriam K., Walker, Jerilyn A., MacArthur, Daniel G., Lek, Monkol, Sudbrak, Herwig, Ralf, Shriver, Mark D., Bustamante, Carlos D., Byrnes, Jake K., De La Vega, Francisco M., Gravel, Simon, Kenny, Eimear E., Kidd, Jeffrey M., Lacroute, Phil, Maples, Brian K., Moreno-Estrada, Andres, Zakharia, Fouad, Halperin, Eran, Baran, Yael, Craig, David W., Christoforides, Alexis, Homer, Nils, Izatt, Tyler, Kurdoglu, Ahmet A., Sinari, Shripad A., Squire, Kevin, Xiao, Chunlin, Sebat, Jonathan, Bafna, Vineet, Ye, Kenny, Burchard, Esteban G., Hernandez, Ryan D., Gignoux, Christopher R., Haussler, David, Katzman, Sol J., James Kent, W., Howie, Bryan, Ruiz-Linares, Andres, Dermitzakis, Emmanouil T., Lappalainen, Tuuli, Devine, Scott E., Liu, Xinyue, Maroo, Ankit, Tallon, Luke J., Rosenfeld, Jeffrey A., Min Kang, Hyun, Anderson, Paul, Angius, Andrea, Bigham, Abigail, Blackwell, Tom, Busonero, Fabio, Cucca, Francesco, Fuchsberger, Christian, Jones, Chris, Jun, Goo, Li, Yun, Lyons, Robert, Maschio, Andrea, Porcu, Eleonora, Reinier, Fred, Sanna, Serena, Schlessinger, David, Sidore, Carlo, Tan, Adrian, Kate Trost, Mary, Awadalla, Philip, Hodgkinson, Alan, Lunter, Gerton, McVean, Gil A., Marchini, Jonathan L., Myers, Simon, Churchhouse, Claire, Delaneau, Olivier, Gupta-Hinch, Anjali, Iqbal, Zamin, Mathieson, Iain, Rimmer, Andy, Xifara, Dionysia K., Oleksyk, Taras K., Fu, Yunxin, Liu, Xiaoming, Xiong, Momiao, Jorde, Lynn, Witherspoon, David, Xing, Jinchuan, Eichler, Evan E., Browning, Brian L., Alkan, Can, Hajirasouliha, Iman, Hormozdiari, Fereydoun, Ko, Arthur, Sudmant, Peter H., Mardis, Elaine R., Chen, Ken, Chinwalla, Asif, Ding, Li, Dooling, David, Koboldt, Daniel C., McLellan, Michael D., Wallis, John W., Wendl, Michael C., Zhang, Qunyuan, Hurles, Matthew E., Tyler-Smith, Chris, Albers, Cornelis A., Ayub, Qasim, Chen, Yuan, Coffey, Alison J., Colonna, Vincenza, Huang, Ni, Jostins, Luke, Li, Heng, Scally, Aylwyn, Walter, Klaudia, Xue, Yali, Zhang, Yujun, Gerstein, Mark B., Abyzov, Alexej, Balasubramanian, Suganthi, Chen, Jieming, Clarke, Declan, Fu, Yao, Habegger, Lukas, Harmanci, Arif O., Jin, Mike, Khurana, Ekta, Jasmine Mu, Xinmeng, Sisu, Cristina, Lee, Charles, McCarroll, Steven A., Degenhardt, Jeremiah, Korbel, Jan O., Stütz, Adrian M., Church, Deanna, Michaelson, Jacob J., Eichler, Evan E., Hurles, Matthew E., Blackburne, Ben, Lindsay, Sarah J., Ning, Zemin, DePristo, Mark A., Min Kang, Hyun, Mardis, Elaine R., Yu, Fuli, Michelson, Leslie P., Tyler-Smith, Chris, Frankish, Adam, Harrow, Jennifer, Fowler, Gerald, Hale, Walker, Kalra, Divya, Flicek, Paul, Clarke, Laura, Barker, Jonathan, Kelman, Gavin, Kulesha, Eugene, Radhakrishnan, Rajesh, Roa, Asier, Smirnov, Dmitriy, Streeter, Ian, Toneva, Iliana, Vaughan, Brendan, Sherry, Stephen T., Ananiev, Victor, Belaia, Zinaida, Beloslyudtsev, Dimitriy, Bouk, Nathan, Chen, Chao, Cohen, Robert, Cook, Charles, Garner, John, Hefferon, Timothy, Kimelman, Mikhail, Liu, Chunlei, Lopez, John, Meric, Peter, OʼSullivan, Chris, Ostapchuk, Yuri, Phan, Lon, Ponomarov, Sergiy, Schneider, Valerie, Shekhtman, Eugene, Sirotkin, Karl, Slotta, Douglas, Zhang, Hua, Chakravarti, Aravinda, Knoppers, Bartha M., Barnes, Kathleen C., Beiswanger, Christine, Burchard, Esteban G., Bustamante, Carlos D., Cai, Hongyu, Cao, Hongzhi, Durbin, Richard M., Gharani, Neda, Henn, Brenna, Jones, Danielle, Jorde, Lynn, Kaye, Jane S., Kent, Alastair, Kerasidou, Angeliki, Mathias, Rasika, Ossorio, Pilar N., Parker, Michael, Reich, David, Rotimi, Charles N., Royal, Charmaine D., Sandoval, Karla, Su, Yeyang, Sudbrak, Ralf, Tian, Zhongming, Tishkoff, Sarah, Toji, Lorraine H., Tyler-Smith, Chris, Via, Marc, Wang, Yuhong, Yang, Huanming, Yang, Ling, Zhu, Jiayong, Bodmer, Walter, Bedoya, Gabriel, Ruiz-Linares, Andres, Zhi Ming, Cai, Yang, Gao, Jia You, Chu, Peltonen, Leena, Garcia-Montero, Andres, Orfao, Alberto, Dutil, Julie, Martinez-Cruzado, Juan C., Oleksyk, Taras K., Brooks, Lisa D., Felsenfeld, Adam L., McEwen, Jean E., Clemm, Nicholas C., Duncanson, Audrey, Dunn, Michael, Guyer, Mark S., Peterson, Jane L., Abecasis, Goncalo R., and Auton, Adam

Published
2012
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9. Genotyping Array Design and Data Quality Control in the Million Veteran Program

Author

Hunter-Zinck, Haley, primary, Shi, Yunling, additional, Li, Man, additional, Gorman, Bryan R., additional, Ji, Sun-Gou, additional, Sun, Ning, additional, Webster, Teresa, additional, Liem, Andrew, additional, Hsieh, Paul, additional, Devineni, Poornima, additional, Karnam, Purushotham, additional, Gong, Xin, additional, Radhakrishnan, Lakshmi, additional, Schmidt, Jeanette, additional, Assimes, Themistocles L., additional, Huang, Jie, additional, Pan, Cuiping, additional, Humphries, Donald, additional, Brophy, Mary, additional, Moser, Jennifer, additional, Muralidhar, Sumitra, additional, Huang, Grant D., additional, Przygodzki, Ronald, additional, Concato, John, additional, Gaziano, John M., additional, Gelernter, Joel, additional, O’Donnell, Christopher J., additional, Hauser, Elizabeth R., additional, Zhao, Hongyu, additional, O’Leary, Timothy J., additional, Tsao, Philip S., additional, and Pyarajan, Saiju, additional

Published
2020
Full Text
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12. Algorithms for large-scale genotyping microarrays

Author

Liu, Wei-min, Di, Xiaojun, Yang, Geoffrey, Matsauzaki, Hajime, Huang, Jing, Mei, Rui, Ryder, Thomas B., Webster, Teresa A., Dong, Shoulian, Liu, Guoying, Jones, Keith W., Kennedy, Giulia C., and Kulp, David

Published
2003

14. High‐density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

Author

Winfield, Mark O., Allen, Alexandra M., Burridge, Amanda J., Barker, Gary L. A., Benbow, Harriet R., Wilkinson, Paul A., Coghill, Jane, Waterfall, Christy, Davassi, Alessandro, Scopes, Geoff, Pirani, Ali, Webster, Teresa, Brew, Fiona, Bloor, Claire, King, Julie, West, Claire, Griffiths, Simon, King, Ian, Bentley, Alison R., and Edwards, Keith J.

Subjects
Genetic Markers, Genotype, Genotyping Techniques, wheat progenitors, food and beverages, next‐generation sequencing, Genetic Variation, Gene Pool, Breeding, Polymorphism, Single Nucleotide, genotyping array, Polyploidy, secondary and tertiary gene pools, single nucleotide polymorphism, wheat, Research Articles, Genome, Plant, Triticum, Research Article, Oligonucleotide Array Sequence Analysis
Abstract

Summary In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra‐high‐density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.

Published
2015

15. The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine

Author

Elhaik, Eran, primary, Yusuf, Leeban, additional, Anderson, Ainan I J, additional, Pirooznia, Mehdi, additional, Arnellos, Dimitrios, additional, Vilshansky, Gregory, additional, Ercal, Gunes, additional, Lu, Yontao, additional, Webster, Teresa, additional, Baird, Michael L, additional, and Esposito, Umberto, additional

Published
2017
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16. High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

Author

Winfield, Mark O, Allen, Alexandra M, Burridge, Amanda J, Barker, Gary L A, Benbow, Harriet R, Wilkinson, Paul A, Coghill, Jane, Waterfall, Christy, Davassi, Alessandro, Scopes, Geoff, Pirani, Ali, Webster, Teresa, Brew, Fiona, Bloor, Claire, King, Julie, West, Claire, Griffiths, Simon, King, Ian, Bentley, Alison R, and Edwards, Keith J

Subjects
food and beverages
Abstract

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site.

Published
2016

17. Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum)

Author

Allen, Alexandra M., primary, Winfield, Mark O., additional, Burridge, Amanda J., additional, Downie, Rowena C., additional, Benbow, Harriet R., additional, Barker, Gary L. A., additional, Wilkinson, Paul A., additional, Coghill, Jane, additional, Waterfall, Christy, additional, Davassi, Alessandro, additional, Scopes, Geoff, additional, Pirani, Ali, additional, Webster, Teresa, additional, Brew, Fiona, additional, Bloor, Claire, additional, Griffiths, Simon, additional, Bentley, Alison R., additional, Alda, Mark, additional, Jack, Peter, additional, Phillips, Andrew L., additional, and Edwards, Keith J., additional

Published
2016
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18. Additional file 2: Figure S1. of Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Author

Li, Yun, Setten, Jessica Van, Verma, Shefali, Yontao Lu, Holmes, Michael, Gao, Hui, Monkol Lek, Nair, Nikhil, Hareesh Chandrupatla, Baoli Chang, Karczewski, Konrad, Wong, Chanel, Maede Mohebnasab, Eyas Mukhtar, Phillips, Randy, Tragante, Vinicius, Cuiping Hou, Steel, Laura, Takesha Lee, Garifallou, James, Toumy Guettouche, Hongzhi Cao, Weihua Guan, Himes, Aubree, Houten, Jacob Van, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael, Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey, McGinn, Daniel, Abhinav Gangasani, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Tiancheng Wang, Baolin Wu, Alhusain Alzahrani, Amein Al-Ali, Al-Muhanna, Fahad, Al-Rubaish, Abdullah, Al-Mueilo, Samir, Monos, Dimitri, Murphy, Barbara, Olthoff, Kim, Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Suganthi Balasubramanian, Lanktree, Matthew, Oetting, William, Garcia-Pavia, Pablo, MacArthur, Daniel, Bakker, Paul De, Hakon Hakonarson, Birdwell, Kelly, Jacobson, Pamala, Ritchie, Marylyn, Asselbergs, Folkert, Israni, Ajay, Shaked, Abraham, and Keating, Brendan

Abstract

TxArray transplant-specific modular contents. (PDF 140 kb)

Published
2015
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19. Additional file 1: Table S1. of Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Author

Li, Yun, Setten, Jessica Van, Verma, Shefali, Yontao Lu, Holmes, Michael, Gao, Hui, Monkol Lek, Nair, Nikhil, Hareesh Chandrupatla, Baoli Chang, Karczewski, Konrad, Wong, Chanel, Maede Mohebnasab, Eyas Mukhtar, Phillips, Randy, Tragante, Vinicius, Cuiping Hou, Steel, Laura, Takesha Lee, Garifallou, James, Toumy Guettouche, Hongzhi Cao, Weihua Guan, Himes, Aubree, Houten, Jacob Van, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael, Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey, McGinn, Daniel, Abhinav Gangasani, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Tiancheng Wang, Baolin Wu, Alhusain Alzahrani, Amein Al-Ali, Al-Muhanna, Fahad, Al-Rubaish, Abdullah, Al-Mueilo, Samir, Monos, Dimitri, Murphy, Barbara, Olthoff, Kim, Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Suganthi Balasubramanian, Lanktree, Matthew, Oetting, William, Garcia-Pavia, Pablo, MacArthur, Daniel, Bakker, Paul De, Hakon Hakonarson, Birdwell, Kelly, Jacobson, Pamala, Ritchie, Marylyn, Asselbergs, Folkert, Israni, Ajay, Shaked, Abraham, and Keating, Brendan

Abstract

Tagging and coverage of MHC region markers. Table S2: Tagging and coverage of Tx-specific genes. Table S3: Untranslated regions (UTRs) considered in the TxArray design. Table S4: Loss-of-function variants included in the TxArray. Table S5: Copy number polymorphisms (CNPs) and variations (CNVs) included in the TxArray. (DOCX 54 kb)

Published
2015
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20. Development and preliminary evaluation of the IStraw90 Axiom® array in the cultivated strawberry (Fragaria × ananassa)

Author

Bassil, Nahla, Davis, Thomas, Amaya, Iraida, Bellon, Laurent, Brew, Fiona, DENOYES, Beatrice, van Dijk, Thijs, Ficklin, Stephen, Lezzoni, Amy, Jung, Sook, Mahoney, Lise L., Main, Dorrie, Mittmann, Michael, Monfort, Amparo, Peace, Cameron, Pirani, Ali, Rosyara, Umesh, Sargent, Daniel J., Webster, Teresa A., Wood, Dave J., Yang, Y., Zhang, Hailong, Van de Weg, W. Eric, ARS, University of New Hampshire (UNH), Instituto Andaluz de Investigación y Formación Agraria y Pesquera (IFAPA), Affymetrix Inc., Affymetrix UK Ltd, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Wageningen University and Research Centre (WUR), Washington State University (WSU), Michigan State University [East Lansing], Michigan State University System, Institute of Agrifood Research and Technology (IRTA), Centro Ricerca e Innovazione, Fondazione Edmund Mach, Instituto Agrario S. Michele all' Adige, and ProdInra, Migration

Subjects
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

21. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Author

Li, Yun R., van Setten, Jessica, Verma, Shefali S., Lu, Yontao, Holmes, Michael V., Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad J., Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael B., Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey M., McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain J., Al-Ali, Amein K., Al-Muhanna, Fahad A., Al-Rubaish, Abdullah M., Al-Mueilo, Samir, Monos, Dimitri S., Murphy, Barbara, Olthoff, Kim M., Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew B., Oetting, William S., Garcia-Pavia, Pablo, MacArthur, Daniel G., de Bakker, Paul I W, Hakonarson, Hakon, Birdwell, Kelly A., Jacobson, Pamala A., Ritchie, Marylyn D., Asselbergs, Folkert W., Israni, Ajay K., Shaked, Abraham, Keating, Brendan J., Li, Yun R., van Setten, Jessica, Verma, Shefali S., Lu, Yontao, Holmes, Michael V., Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad J., Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael B., Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey M., McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain J., Al-Ali, Amein K., Al-Muhanna, Fahad A., Al-Rubaish, Abdullah M., Al-Mueilo, Samir, Monos, Dimitri S., Murphy, Barbara, Olthoff, Kim M., Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew B., Oetting, William S., Garcia-Pavia, Pablo, MacArthur, Daniel G., de Bakker, Paul I W, Hakonarson, Hakon, Birdwell, Kelly A., Jacobson, Pamala A., Ritchie, Marylyn D., Asselbergs, Folkert W., Israni, Ajay K., Shaked, Abraham, and Keating, Brendan J.

Published
2015

22. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies.

Author

Li, Yun R, van Setten, Jessica, Verma, Shefali S, Lu, Yontao, Holmes, Michael V, Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad J, Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael B, Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey M, McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain J, Al-Ali, Amein K, Al-Muhanna, Fahad A, Al-Rubaish, Abdullah M, Al-Mueilo, Samir, Monos, Dimitri S, Murphy, Barbara, Olthoff, Kim M, Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew B, Oetting, William S, Garcia-Pavia, Pablo, MacArthur, Daniel G, de Bakker, Paul IW, Hakonarson, Hakon, Birdwell, Kelly A, Jacobson, Pamala A, Ritchie, Marylyn D, Asselbergs, Folkert W, Israni, Ajay K, Shaked, Abraham, Keating, Brendan J, Li, Yun R, van Setten, Jessica, Verma, Shefali S, Lu, Yontao, Holmes, Michael V, Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad J, Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael B, Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey M, McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain J, Al-Ali, Amein K, Al-Muhanna, Fahad A, Al-Rubaish, Abdullah M, Al-Mueilo, Samir, Monos, Dimitri S, Murphy, Barbara, Olthoff, Kim M, Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew B, Oetting, William S, Garcia-Pavia, Pablo, MacArthur, Daniel G, de Bakker, Paul IW, Hakonarson, Hakon, Birdwell, Kelly A, Jacobson, Pamala A, Ritchie, Marylyn D, Asselbergs, Folkert W, Israni, Ajay K, Shaked, Abraham, and Keating, Brendan J

Abstract

BACKGROUND: In addition to HLA genetic incompatibility, non-HLA difference between donor and recipients of transplantation leading to allograft rejection are now becoming evident. We aimed to create a unique genome-wide platform to facilitate genomic research studies in transplant-related studies. We designed a genome-wide genotyping tool based on the most recent human genomic reference datasets, and included customization for known and potentially relevant metabolic and pharmacological loci relevant to transplantation. METHODS: We describe here the design and implementation of a customized genome-wide genotyping array, the 'TxArray', comprising approximately 782,000 markers with tailored content for deeper capture of variants across HLA, KIR, pharmacogenomic, and metabolic loci important in transplantation. To test concordance and genotyping quality, we genotyped 85 HapMap samples on the array, including eight trios. RESULTS: We show low Mendelian error rates and high concordance rates for HapMap samples (average parent-parent-child heritability of 0.997, and concordance of 0.996). We performed genotype imputation across autosomal regions, masking directly genotyped SNPs to assess imputation accuracy and report an accuracy of >0.962 for directly genotyped SNPs. We demonstrate much higher capture of the natural killer cell immunoglobulin-like receptor (KIR) region versus comparable platforms. Overall, we show that the genotyping quality and coverage of the TxArray is very high when compared to reference samples and to other genome-wide genotyping platforms. CONCLUSIONS: We have designed a comprehensive genome-wide genotyping tool which enables accurate association testing and imputation of ungenotyped SNPs, facilitating powerful and cost-effective large-scale genotyping of transplant-related studies.

Published
2015

23. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Author

Experimentele Afd. Cardiologie 1, Circulatory Health, Infection & Immunity, JC onderzoeksprogramma Methodologie, Cancer, Cardiologie, Li, Yun R., van Setten, Jessica, Verma, Shefali S., Lu, Yontao, Holmes, Michael V., Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad J., Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael B., Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey M., McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain J., Al-Ali, Amein K., Al-Muhanna, Fahad A., Al-Rubaish, Abdullah M., Al-Mueilo, Samir, Monos, Dimitri S., Murphy, Barbara, Olthoff, Kim M., Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew B., Oetting, William S., Garcia-Pavia, Pablo, MacArthur, Daniel G., de Bakker, Paul I W, Hakonarson, Hakon, Birdwell, Kelly A., Jacobson, Pamala A., Ritchie, Marylyn D., Asselbergs, Folkert W., Israni, Ajay K., Shaked, Abraham, Keating, Brendan J., Experimentele Afd. Cardiologie 1, Circulatory Health, Infection & Immunity, JC onderzoeksprogramma Methodologie, Cancer, Cardiologie, Li, Yun R., van Setten, Jessica, Verma, Shefali S., Lu, Yontao, Holmes, Michael V., Gao, Hui, Lek, Monkol, Nair, Nikhil, Chandrupatla, Hareesh, Chang, Baoli, Karczewski, Konrad J., Wong, Chanel, Mohebnasab, Maede, Mukhtar, Eyas, Phillips, Randy, Tragante, Vinicius, Hou, Cuiping, Steel, Laura, Lee, Takesha, Garifallou, James, Guettouche, Toumy, Cao, Hongzhi, Guan, Weihua, Himes, Aubree, van Houten, Jacob, Pasquier, Andrew, Yu, Reina, Carrigan, Elena, Miller, Michael B., Schladt, David, Akdere, Abdullah, Gonzalez, Ana, Llyod, Kelsey M., McGinn, Daniel, Gangasani, Abhinav, Michaud, Zach, Colasacco, Abigail, Snyder, James, Thomas, Kelly, Wang, Tiancheng, Wu, Baolin, Alzahrani, Alhusain J., Al-Ali, Amein K., Al-Muhanna, Fahad A., Al-Rubaish, Abdullah M., Al-Mueilo, Samir, Monos, Dimitri S., Murphy, Barbara, Olthoff, Kim M., Wijmenga, Cisca, Webster, Teresa, Kamoun, Malek, Balasubramanian, Suganthi, Lanktree, Matthew B., Oetting, William S., Garcia-Pavia, Pablo, MacArthur, Daniel G., de Bakker, Paul I W, Hakonarson, Hakon, Birdwell, Kelly A., Jacobson, Pamala A., Ritchie, Marylyn D., Asselbergs, Folkert W., Israni, Ajay K., Shaked, Abraham, and Keating, Brendan J.

Published
2015

24. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

Author

Department of Agriculture (US), National Research Initiative (US), Ministerio de Ciencia e Innovación (España), Bassil, Nahla, Davis, T. M., Zhang, Hailong, Ficklin, Stephen, Mittmann, Mike, Webster, Teresa, Mahoney, Lise, Wood, David, Alperin, Elisabeth S., Rosyara, Umesh R., Koehorst-van Putten, Herma J. J., Monfort, Amparo, Sargent, Daniel J., Amaya, Iraida, Denoyes, Béatrice, Bianco, Luca, Dijk, Thijs van, Pirani, Ali, Iezzoni, Amy, Main, Dorrie, Peace, Cameron, Yang, Yilong, Whitaker, Vance M., Verma, Sujeet, Bellon, Laurent, Brew, Fiona, Herrera, Raul, Weg, Eric van de, Department of Agriculture (US), National Research Initiative (US), Ministerio de Ciencia e Innovación (España), Bassil, Nahla, Davis, T. M., Zhang, Hailong, Ficklin, Stephen, Mittmann, Mike, Webster, Teresa, Mahoney, Lise, Wood, David, Alperin, Elisabeth S., Rosyara, Umesh R., Koehorst-van Putten, Herma J. J., Monfort, Amparo, Sargent, Daniel J., Amaya, Iraida, Denoyes, Béatrice, Bianco, Luca, Dijk, Thijs van, Pirani, Ali, Iezzoni, Amy, Main, Dorrie, Peace, Cameron, Yang, Yilong, Whitaker, Vance M., Verma, Sujeet, Bellon, Laurent, Brew, Fiona, Herrera, Raul, and Weg, Eric van de

Abstract

[Background]: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array., [Results]: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM., [Conclusions]: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.

Published
2015

25. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

Author

Bassil, N.V., Davis, T.M., Zhang, Hailong, Ficklin, Stephen, Mittmann, Mike, Webster, Teresa, Mahoney, Lise, Wood, David, Alperin, E.S., Rosyara, U.R., Koehorst-vanc Putten, Herma, Monfort, Amparo, Sargent, D.J., Amaya, Iraida, Denoyes, Beatrice, Bianco, Luca, van Dijk, Thijs, Pirani, Ali, Iezzoni, Amy, Main, Dorrie, Peace, Cameron, Yang, Yilong, Whitaker, Vance, Verma, Sujeet, Bellon, Laurent, Brew, Fiona, Herrera, Raul, van de Weg, Eric, Bassil, N.V., Davis, T.M., Zhang, Hailong, Ficklin, Stephen, Mittmann, Mike, Webster, Teresa, Mahoney, Lise, Wood, David, Alperin, E.S., Rosyara, U.R., Koehorst-vanc Putten, Herma, Monfort, Amparo, Sargent, D.J., Amaya, Iraida, Denoyes, Beatrice, Bianco, Luca, van Dijk, Thijs, Pirani, Ali, Iezzoni, Amy, Main, Dorrie, Peace, Cameron, Yang, Yilong, Whitaker, Vance, Verma, Sujeet, Bellon, Laurent, Brew, Fiona, Herrera, Raul, and van de Weg, Eric

Abstract

A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. Results: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing "haploSNPs" (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative "codon-based" SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix's "SNPolisher" R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family 'Holiday' × 'Korona' with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. Conclusions: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array's high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyse

Published
2015

26. ARIADNE: PATTERN-DIRECTED INFERENCE AND HIERARCHICAL ABSTRACTION IN PROTEIN STRUCTURE RECOGNITION.

Author

Lathrop, Richard H., Webster, Teresa A., and Smith, Temple F.

Subjects
*PROTEINS, *MICROELECTRONICS, *CELLS, *HYDROPHOBIC surfaces, *MOLECULAR structure, *MICROPROCESSORS
Abstract

This article focuses on hierarchical abstraction in the protein structure recognition. The system ARIADNE identifies the optimal match between a given complex pattern descriptor and genetic (protein) sequences annotated with various inferred properties, by abstracting intermediate levels of structural organization. Inference is grounded solely in knowledge derivable from the primary sequence, and exploits such weakly inferred properties as secondary structure predictions and hydrophobicity. There are many situations in which a detailed low level description encodes, through a hierarchical organization, a recognizable higher-order pattern. For example, in the micro-world of VLSI integrated circuits, transistors are organized into inverters, inverters into register cells, register cells into register banks, and so on up to microprocessor. Recognition of a hierarchical organization from low level detail proceeds most naturally by hierarchical construction of the intervening patterns.

Published
1987
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27. Concept and design of a genome-wide association genotyping array tailored for transplantation-specific studies

Author

Li, Yun R., primary, van Setten, Jessica, additional, Verma, Shefali S., additional, Lu, Yontao, additional, Holmes, Michael V., additional, Gao, Hui, additional, Lek, Monkol, additional, Nair, Nikhil, additional, Chandrupatla, Hareesh, additional, Chang, Baoli, additional, Karczewski, Konrad J., additional, Wong, Chanel, additional, Mohebnasab, Maede, additional, Mukhtar, Eyas, additional, Phillips, Randy, additional, Tragante, Vinicius, additional, Hou, Cuiping, additional, Steel, Laura, additional, Lee, Takesha, additional, Garifallou, James, additional, Guettouche, Toumy, additional, Cao, Hongzhi, additional, Guan, Weihua, additional, Himes, Aubree, additional, van Houten, Jacob, additional, Pasquier, Andrew, additional, Yu, Reina, additional, Carrigan, Elena, additional, Miller, Michael B., additional, Schladt, David, additional, Akdere, Abdullah, additional, Gonzalez, Ana, additional, Llyod, Kelsey M., additional, McGinn, Daniel, additional, Gangasani, Abhinav, additional, Michaud, Zach, additional, Colasacco, Abigail, additional, Snyder, James, additional, Thomas, Kelly, additional, Wang, Tiancheng, additional, Wu, Baolin, additional, Alzahrani, Alhusain J., additional, Al-Ali, Amein K., additional, Al-Muhanna, Fahad A., additional, Al-Rubaish, Abdullah M., additional, Al-Mueilo, Samir, additional, Monos, Dimitri S., additional, Murphy, Barbara, additional, Olthoff, Kim M., additional, Wijmenga, Cisca, additional, Webster, Teresa, additional, Kamoun, Malek, additional, Balasubramanian, Suganthi, additional, Lanktree, Matthew B., additional, Oetting, William S., additional, Garcia-Pavia, Pablo, additional, MacArthur, Daniel G., additional, de Bakker, Paul I W, additional, Hakonarson, Hakon, additional, Birdwell, Kelly A., additional, Jacobson, Pamala A., additional, Ritchie, Marylyn D., additional, Asselbergs, Folkert W., additional, Israni, Ajay K., additional, Shaked, Abraham, additional, and Keating, Brendan J., additional

Published
2015
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28. Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa

Author

Bassil, Nahla V, primary, Davis, Thomas M, additional, Zhang, Hailong, additional, Ficklin, Stephen, additional, Mittmann, Mike, additional, Webster, Teresa, additional, Mahoney, Lise, additional, Wood, David, additional, Alperin, Elisabeth S, additional, Rosyara, Umesh R, additional, Koehorst-vanc Putten, Herma, additional, Monfort, Amparo, additional, Sargent, Daniel J, additional, Amaya, Iraida, additional, Denoyes, Beatrice, additional, Bianco, Luca, additional, van Dijk, Thijs, additional, Pirani, Ali, additional, Iezzoni, Amy, additional, Main, Dorrie, additional, Peace, Cameron, additional, Yang, Yilong, additional, Whitaker, Vance, additional, Verma, Sujeet, additional, Bellon, Laurent, additional, Brew, Fiona, additional, Herrera, Raul, additional, and van de Weg, Eric, additional

Published
2015
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29. Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat ( Triticum aestivum).

Author

Allen, Alexandra M., Winfield, Mark O., Burridge, Amanda J., Downie, Rowena C., Benbow, Harriet R., Barker, Gary L. A., Wilkinson, Paul A., Coghill, Jane, Waterfall, Christy, Davassi, Alessandro, Scopes, Geoff, Pirani, Ali, Webster, Teresa, Brew, Fiona, Bloor, Claire, Griffiths, Simon, Bentley, Alison R., Alda, Mark, Jack, Peter, and Phillips, Andrew L.

Subjects
SINGLE nucleotide polymorphisms, WHEAT genetics, WHEAT breeding, GENOTYPES, MICROPLATES
Abstract

Targeted selection and inbreeding have resulted in a lack of genetic diversity in elite hexaploid bread wheat accessions. Reduced diversity can be a limiting factor in the breeding of high yielding varieties and crucially can mean reduced resilience in the face of changing climate and resource pressures. Recent technological advances have enabled the development of molecular markers for use in the assessment and utilization of genetic diversity in hexaploid wheat. Starting with a large collection of 819 571 previously characterized wheat markers, here we describe the identification of 35 143 single nucleotide polymorphism-based markers, which are highly suited to the genotyping of elite hexaploid wheat accessions. To assess their suitability, the markers have been validated using a commercial high-density Affymetrix Axiom® genotyping array (the Wheat Breeders' Array), in a high-throughput 384 microplate configuration, to characterize a diverse global collection of wheat accessions including landraces and elite lines derived from commercial breeding communities. We demonstrate that the Wheat Breeders' Array is also suitable for generating high-density genetic maps of previously uncharacterized populations and for characterizing novel genetic diversity produced by mutagenesis. To facilitate the use of the array by the wheat community, the markers, the associated sequence and the genotype information have been made available through the interactive web site 'CerealsDB'. [ABSTRACT FROM AUTHOR]

Published
2017
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30. Evidence for dispensable sequences inserted into a nucleotide fold

Author

Starzyk, Ruth M., Webster, Teresa A., and Schimmel, Paul

Subjects
Genetic engineering -- Research -- Analysis, Amino acid sequence -- Analysis -- Research, Transfer RNA -- Research -- Analysis, Escherichia coli -- Research -- Analysis, Science and technology, Analysis, Research
Abstract

Evidence for Dispensable Sequences Inserted into a Nucleotide Fold IT IS POSSIBLE TO DISSECT PROTEINS into pieces and to investigate activities and structures of fragments (1-3). The delineation of substructures [...]

Published
1987

31. High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

Author

Winfield, Mark O., Allen, Alexandra M., Burridge, Amanda J., Barker, Gary L. A., Benbow, Harriet R., Wilkinson, Paul A., Coghill, Jane, Waterfall, Christy, Davassi, Alessandro, Scopes, Geoff, Pirani, Ali, Webster, Teresa, Brew, Fiona, Bloor, Claire, King, Julie, West, Claire, Griffiths, Simon, King, Ian, Bentley, Alison R., and Edwards, Keith J.

Subjects
SINGLE nucleotide polymorphisms, WHEAT genetics, GENETIC markers, DIPLOIDY, CROP yields
Abstract

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom® genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site. [ABSTRACT FROM AUTHOR]

Published
2016
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32. Ancient Admixture in Human History

Author

Patterson, Nick, primary, Moorjani, Priya, additional, Luo, Yontao, additional, Mallick, Swapan, additional, Rohland, Nadin, additional, Zhan, Yiping, additional, Genschoreck, Teri, additional, Webster, Teresa, additional, and Reich, David, additional

Published
2012
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33. ARIADNE: Pattern-Directed Inference and Hierarchical Abstraction in Protein Structure Recognition

Author

Lathrop, Richard H., Webster, Teresa A., Smith, Temple F., Lathrop, Richard H., Webster, Teresa A., and Smith, Temple F.

Abstract

There are many situations in which a very detailed low-level description encodes, through a hierarchical organization, a recognizable higher-order pattern. The macro-molecular structural conformations of proteins exhibit higher order regularities whose recognition is complicated by many factors. ARIADNE searches for similarities between structural descriptors and hypothesized protein structure at levels more abstract than the primary sequence, based on differential similarity to rule antecedents and the controlled use of tentative higher-order structural hypotheses. Inference is grounded solely in knowledge derivable from the primary sequence, and exploits secondary structure predictions. A novel proposed alignment and functional domain identification of the aminoacyl-tRNA synthetases was found using this system.

Published
2004

34. Design and coverage of high throughput genotyping arrays optimized for individuals of East Asian, African American, and Latino race/ethnicity using imputation and a novel hybrid SNP selection algorithm

Author

Hoffmann, Thomas J., primary, Zhan, Yiping, additional, Kvale, Mark N., additional, Hesselson, Stephanie E., additional, Gollub, Jeremy, additional, Iribarren, Carlos, additional, Lu, Yontao, additional, Mei, Gangwu, additional, Purdy, Matthew M., additional, Quesenberry, Charles, additional, Rowell, Sarah, additional, Shapero, Michael H., additional, Smethurst, David, additional, Somkin, Carol P., additional, Van den Eeden, Stephen K., additional, Walter, Larry, additional, Webster, Teresa, additional, Whitmer, Rachel A., additional, Finn, Andrea, additional, Schaefer, Catherine, additional, Kwok, Pui-Yan, additional, and Risch, Neil, additional

Published
2011
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35. Next generation genome-wide association tool: Design and coverage of a high-throughput European-optimized SNP array

Author

Hoffmann, Thomas J., primary, Kvale, Mark N., additional, Hesselson, Stephanie E., additional, Zhan, Yiping, additional, Aquino, Christine, additional, Cao, Yang, additional, Cawley, Simon, additional, Chung, Elaine, additional, Connell, Sheryl, additional, Eshragh, Jasmin, additional, Ewing, Marcia, additional, Gollub, Jeremy, additional, Henderson, Mary, additional, Hubbell, Earl, additional, Iribarren, Carlos, additional, Kaufman, Jay, additional, Lao, Richard Z., additional, Lu, Yontao, additional, Ludwig, Dana, additional, Mathauda, Gurpreet K., additional, McGuire, William, additional, Mei, Gangwu, additional, Miles, Sunita, additional, Purdy, Matthew M., additional, Quesenberry, Charles, additional, Ranatunga, Dilrini, additional, Rowell, Sarah, additional, Sadler, Marianne, additional, Shapero, Michael H., additional, Shen, Ling, additional, Shenoy, Tanushree R., additional, Smethurst, David, additional, Van den Eeden, Stephen K., additional, Walter, Larry, additional, Wan, Eunice, additional, Wearley, Reid, additional, Webster, Teresa, additional, Wen, Christopher C., additional, Weng, Li, additional, Whitmer, Rachel A., additional, Williams, Alan, additional, Wong, Simon C., additional, Zau, Chia, additional, Finn, Andrea, additional, Schaefer, Catherine, additional, Kwok, Pui-Yan, additional, and Risch, Neil, additional

Published
2011
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36. Integrated detection and population-genetic analysis of SNPs and copy number variation

Author

McCarroll, Steven A, primary, Kuruvilla, Finny G, additional, Korn, Joshua M, additional, Cawley, Simon, additional, Nemesh, James, additional, Wysoker, Alec, additional, Shapero, Michael H, additional, de Bakker, Paul I W, additional, Maller, Julian B, additional, Kirby, Andrew, additional, Elliott, Amanda L, additional, Parkin, Melissa, additional, Hubbell, Earl, additional, Webster, Teresa, additional, Mei, Rui, additional, Veitch, James, additional, Collins, Patrick J, additional, Handsaker, Robert, additional, Lincoln, Steve, additional, Nizzari, Marcia, additional, Blume, John, additional, Jones, Keith W, additional, Rava, Rich, additional, Daly, Mark J, additional, Gabriel, Stacey B, additional, and Altshuler, David, additional

Published
2008
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37. Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

Author

Matsuzaki, Hajime, primary, Dong, Shoulian, additional, Loi, Halina, additional, Di, Xiaojun, additional, Liu, Guoying, additional, Hubbell, Earl, additional, Law, Jane, additional, Berntsen, Tam, additional, Chadha, Monica, additional, Hui, Henry, additional, Yang, Geoffrey, additional, Kennedy, Giulia C, additional, Webster, Teresa A, additional, Cawley, Simon, additional, Walsh, P Sean, additional, Jones, Keith W, additional, Fodor, Stephen P A, additional, and Mei, Rui, additional

Published
2004
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39. Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase

Author

Webster, Teresa, Tsai, Hsin, Kula, Maria, Mackie, George A., and Schimmel, Paul

Subjects
Biochemistry -- Research, Microbial enzymes -- Research, Escherichia coli -- Research, Homology (Biology) -- Research, Science and technology, Research
Abstract

Specific Sequence Homology and Three-Dimensional Stucture of an Aminoacyl Transfer RNA Synthetase Aminoacyl transfer RNA (tRNA) synthetases presumably arose early in evolution and established the rules of the genetic code [...]

Published
1984

47. Dynamic model based algorithms for screening and genotyping over 100 K SNPs on oligonucleotide microarrays.

Author

Di X, Matsuzaki H, Webster TA, Hubbell E, Liu G, Dong S, Bartell D, Huang J, Chiles R, Yang G, Shen MM, Kulp D, Kennedy GC, Mei R, Jones KW, and Cawley S

Subjects
Computer Simulation, Genotype, Humans, Software, Algorithms, DNA Mutational Analysis methods, Genetic Testing methods, Models, Genetic, Oligonucleotide Array Sequence Analysis methods, Polymorphism, Single Nucleotide genetics, Sequence Alignment methods, Sequence Analysis, DNA methods
Abstract

Motivation: A high density of single nucleotide polymorphism (SNP) coverage on the genome is desirable and often an essential requirement for population genetics studies. Region-specific or chromosome-specific linkage studies also benefit from the availability of as many high quality SNPs as possible. The availability of millions of SNPs from both Perlegen and the public domain and the development of an efficient microarray-based assay for genotyping SNPs has brought up some interesting analytical challenges. Effective methods for the selection of optimal subsets of SNPs spanning the genome and methods for accurately calling genotypes from probe hybridization patterns have enabled the development of a new microarray-based system for robustly genotyping over 100,000 SNPs per sample., Results: We introduce a new dynamic model-based algorithm (DM) for screening over 3 million SNPs and genotyping over 100,000 SNPs. The model is based on four possible underlying states: Null, A, AB and B for each probe quartet. We calculate a probe-level log likelihood for each model and then select between the four competing models with an SNP-level statistical aggregation across multiple probe quartets to provide a high-quality genotype call along with a quality measure of the call. We assess performance with HapMap reference genotypes, informative Mendelian inheritance relationship in families, and consistency between DM and another genotype classification method. At a call rate of 95.91% the concordance with reference genotypes from the HapMap Project is 99.81% based on over 1.5 million genotypes, the Mendelian error rate is 0.018% based on 10 trios, and the consistency between DM and MPAM is 99.90% at a comparable rate of 97.18%. We also develop methods for SNP selection and optimal probe selection., Availability: The DM algorithm is available in Affymetrix's Genotyping Tools software package and in Affymetrix's GDAS software package. See http://www.affymetrix.com for further information. 10 K and 100 K mapping array data are available on the Affymetrix website.

Published
2005
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